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Microbio > lecture exam 2 > Flashcards

lecture exam 2 Flashcards

1
Q

electron acceptors in aerobic and anaerobic respiraton

A

aerobic: o2
anaerobic: NO3-, SO42-, CO2, Fe3+, SeO4

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2
Q

besides glycolysis, what are other ways to make 5C -> 6C

A
  1. Embden-Meyerhof
  2. **pentose phosphate/ hexomonophosphate
  3. Entner-Duodoroff
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3
Q

oxidative phosphorylation

A

ETC generates proton motor force –> ATP synthesis

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4
Q

Electron Transport Chain

A
  • building proton gradient outside cell
  • transfer from NADH + FADH2 –> terminal e- acceptor
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5
Q

what drives ATP conversion?

A

changing conformation of proteins using chemical gradient (ETC)

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6
Q

Fermentation

A
  • purpose: to remake oxidized form of NAD+ (NADH –> NAD+)
  • pyruvate used to reduce pH of environment
  • oxidative phosphorlyation doesn’t occur (ATP formed only by SLP)
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7
Q

standard reduction potential

A
  • gets more positive as e- use energy to move protons across membrane
  • more negative to more positive carriers
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8
Q

what bond connects phosphate group and sugar?

A

phosphodiester bond

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9
Q

what bond connects nucleotides?

A

hydrogen bond

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10
Q

what did Meselson-Stahl experiment show?

A

semi-conservative replication

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11
Q

how does DNA relieve stress on itself?

A

supercoiling- folds around on itself

structural uniqueness
* major groove 2.2 nm
* minor groove 1.2 nm

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12
Q

bacterial nucleoid

A

condensed DNA (30-50 loops of DNA) but 1 big circle

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13
Q

supercoiling stress

A
  • constraining supercoils
  • wrapping DNA around proteins
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14
Q

why does DNA have chemical polarity?

A
  • nucleotides are asymmetric
  • 5’ 3’
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15
Q

topoisomerase

A

modulates supercoiling of DNA
Topoisomerase 1
* cuts 1 strand and passes other strand through (changes DNA 1 supercoil at a time)
* relieves torsional stress caused by supercoils
Topoisomerase 2:
* cuts both strands and passes 2 other strands from somewhere else in DNA (change DNA 2 supercoils at a time)
* relieves negative supercoils (siproflaxin)
* ex: gyrase- adds negative supercoils (strands rotate and relive strain of unwinding

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16
Q

strand passage

A

topoisomerase binds to DNA –> breaks both strands –> passed DNA strands through break before resealing

enzyme holds the cut ends of DNA so don’t rotate

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17
Q

unsupercoiled DNA
and
positive vs negative supercoils

A

unsupercoiled: 1 wind for 10 bases
positive: overwinding
negative: underwinding (take more base pairs to get from one end to the other)

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18
Q

supercoils

A

twist and compact DNA

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19
Q

is bacterial DNA neg or pos supercoiled?

A

negative

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20
Q

archaeal topoisomerases

A

introduce positve supercoils

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21
Q

primosome

A

DnaA and DnaB bind to sequence at oriC and initiate replication

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22
Q

DNA helicase

A
  • Dna B
  • unwinds helix at replication fork (breaks HB)
  • melts DNA
  • recruits primase
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23
Q

primase

A
  • DnaG
  • lays down primers of RNA for DNA polymerase
  • forms 3’ OH for DNA to attach
  • recruits clamp loader
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24
Q

DNA polymerase III

A
  • does most of DNA replication 5’–>3’
  • needs primer bc cant prime itself
  • 3’ –> 5’ (exonucelase activity for proofreading)
  • 5’ –> 3’ (polymerase activity for DNA synthesis) (Nick translation activity)
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25
Q

DNA polymerase I

A

proof reads
fills in RNA primer gaps
* 5’–> 3’ (exonuclease activity for removal of RNA primer)
* 3’ –> 5’ (exonucelase activity for proofreading)
* 5’ –> 3’ (polymerase activity for DNA synthesis) (Nick translation activity)

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26
Q

RNase H

A

removes RNA primers

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27
Q

DNA ligase

A
  • seals DNA by reforming phosphodiester bonds in backbone
  • links 3’ OH with 5’ phosphate groups
28
Q

SSB

A
  • single-strand DNA binding proteins
  • bind SSDNA @ replication fork and block rejoining
  • makes sure DNA is SS when polymerization machinery is ready to replicate it
29
Q

replication fork

A

where 2 strands are separated and the new synthesis is occuring

30
Q

difference between leading and lagging strand

A

leading: direction of fork along 5->3, polymerase stable on strand
lagging: opposite direction of fork along 3->5, polymerase 3 released and reassembled

31
Q

what structure coordinates activity between leading and lagging strand synthesis?

A

clamp loader

32
Q

plasmids

A

extrachromosomal pieces of DNA

33
Q

low-copy # plasmids

A

1 or 2 copies per cell
ex: F plasmids (from conjugation)

34
Q

high copy # plasmids

A
  • up to 50 copies per cell
  • divide continuously
  • randomly segregate to daughter cells
  • if you have any large DNA fragments
35
Q

thermocyclers

A

hot and cool tubes
take pieces of DNA, identify polymerases, and replicate DNA

36
Q

restriction enzymes

A
  • cut DNA at specific sites
  • normally protect bacteria from viral DNA
37
Q

RNA polymerase

A

binds DNA, reads sequence, polymerasizes RNA

38
Q

sigma factor

A
  • promoter
  • summons RNA polymerase to bind to target DNA sequence
  • 70: guides to most genes
  • 32: active when env problems
  • Bs32: active when stressed by heat
39
Q

what do snRNA and miRNA do?

and type of snRNA

A

regulate transcription

mRNA: splicing in eukaryotes and archaea

40
Q

Aminoacyl tRNA transferase

A

makes charged tRNA meth
esterification

41
Q

what is a ribosome made up of?

A

30s and 50s= 70s

42
Q

what does 23s rRNA do?

A

moves P to A

43
Q

are there more post transcription or translation modifications in bacteria?

A

post-translation

44
Q

what enzymes modify translated proteins?

A
  1. fMet (removed from N-term)
  2. small groups added to a.a. (PO4, CH3, adenylate)
  3. protesases (cleave/ degrade protein)
45
Q

chaperone protein examples

A

GroEl-GroEs complex: chaperone protein that refolds denatured proteins w ATP (Hsp 60 and Hsp 10)

barrel shape- protein to be refolded fits into center or binds to misfoled protein domains

Dnak: Hsp 70 (heat shock) (cant do this on eukaryote cells because too big)

46
Q

sec-dependent pathway

A

secretion pathway that delivers proteins to periplasm

47
Q

signal sequence

A
  • targets ribosome to plasma membrane
  • N-terminal amino acid
  • bound by signal recognition particle (SRP)
48
Q

Type 1 secretion system

A
  • secretes protein out of bacterium
  • type 4 (conjugation)
49
Q

proteases

A

cut proteins at specific amino acid sequences

50
Q

proteasomoes

A

degrade proteins (barrel shape)

51
Q

inducer vs repressor molecules

A

inducer: innactivates repressor (cannot bind to DNA) (lac)
corepressor: activates repressor (binds to DNA) (trp)

both change repressor conformation

52
Q

what sugars make up lactose?

A

glucose and galactose

53
Q

operon
operator
repressor

A

operon: cluster of genes
operator: regulatory site
rep: regulatory protein that blocks mRNA synthesis

54
Q

trpR (repressor) mutants

A
  • unliked: can be put anywhere in organism and will make repressor
  • recessive: can be fixed if you had another WT gene
55
Q

trpOc (operator-constitutive) mutants

A

linked and dominant

56
Q

what is cAMP

A

secondary messenger
mediator of catabolite repression and E. coli

57
Q

what is the activator for Lac transcription?

A

CAP

58
Q

cya gene
vs
crp gene

A

cya: lacks adenylate cyclase (cell can’t grow on fermentable carbon sources other than glucose unless medium has cAMP)
crp: codes for cap

59
Q

horizontal gene transfer

A
  • movement of genes between cells (besides cell division)
  • transformation, conjugation, transduction
60
Q

transposons vs plasmids

A

transposons: carry genes into chromosome
plasmids: carry genes between cells without having to become part of chromosome

61
Q

transition vs transversion point mutations

A

transition: pyrine -> purine
transversion purine-> pyrimidine

62
Q

silent vs missense mutation

A

silent: codes for same aa
missense: changes codon

63
Q

Ames test

A
  • measurement of mutagens
  • uses strain auxotrophic for histidine
  • more colonies: stronger mutagen
64
Q

transformation gene transfer

A
  • DNA uptake from medium
  • competent cells take up exogenous DNA
  • translocasome takes up DNA
65
Q

conjugation gene transfer

A
  • move plasmid from one system to another
  • pilus protein (encoded on F factor) brings 2 cells together
  • in recipient cell, transfered DNA forms new F plasmid
  • Hfr: donor cell
66
Q

transduction gene transfer

A
  • virus transfers genetic material from one bacterium to another
    *
67
Q

defense against transferred DNA

A
  • add methyl groups to DNA bc cut unmeth
  • entering DNA destroyed by endonucleases (unless methylated or from similar species)

Microbio (5 decks)

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